OTT@nyspi.bitnet (jurg) (01/25/91)
Linkage Newsletter Vol. 5 No. 1 January 1991
Published by Jurg Ott, Columbia University, New York (support
through grant HG00008 from the National Center for Human
Genome Research is gratefully acknowledged)
Editorial Assistant: Katherine Montague Tel. (212) 960-2507
Fax: +1-212-568-2750 Bitnet/EARN: OTT@NYSPI
Postal address: Columbia University, Box 58
722 West 168th Street, New York, NY 10032
1. EDITORIAL
This is the fifth year that the Linkage Newsletter is being
published. It appears two to three times a year (but has
occasionally also been issued only once) free of charge. This is
the first time that it is also being distributed by e-mail over
the Bionews electronic network (a brief description of Bionews is
attached to the newsletter when mailed through the postal
system). Individuals wishing to receive the newsletter by postal
mail should write to us.
The purpose of this newsletter is to foster communication
among researchers active in the analysis of human genetic
linkage. The following three paragraphs are quotes from the
first issue in 1987:
1. Basically, the newsletter should readily disseminate pieces
of information relevant to genetic analysis that would not
usually be published in scientific journals, where emphasis is on
linkage analysis. This comprises, for example, proposals for new
methods, notes on computer programs, computer hardware, meetings,
experiences with analysis methods and -- last but not necessarily
least -- gossip.
2. Readers are encouraged to submit articles or notes to be
published in the newsletter, and I will make every effort at
quickly including such contributions. I will not exercise any
censorship, however advertisements for commercial products may
have to be paid for (fee yet to be determined). When announcing
computer programs you will have to specify at what cost they are
available.
3. A Question and Answer section is planned in which I will
discuss questions I have been asked and what I consider as
meaningful answers. Again, contributions from readers to this
section are welcome.
2. LINKAGE COURSES
The third linkage course at Columbia University (an advanced
course) was held November 8-10, 1990. Of the 30 participants, 17
were from the United States and 13 came from other countries
(Australia 1, Belgium 3, Denmark 1, England 3, Finland 2, France
1 Germany 2).
The fourth linkage course at Columbia University will be an
Introductory Course held from May 15-18, 1991 (Wednesday through
Saturday). The previously scheduled dates of April 3-6 had to be
changed because the microcomputer classroom was unavailable then.
Registration is now open and applications will be accepted until
February 28, 1991. An application form is attached to this
newsletter. Please pass on copies of the attached announcement
to anyone interested. There is presently no possibility for
travel stipends or for reduced admission fees. In the fall of
1991, the usual Advanced Linkage Course will be taught at
Columbia University (date not yet set). The topics will include
estimating and testing for heterogeneity; linkage disequilibrium;
linkage with pseudoautosomal loci; risk calculations (also under
linkage disequilibrium and locus heterogeneity).
Linkage courses will also be given in Europe on a more
regular basis. The next European course (an introductory course)
will be held July 9-12, 1991, at the Association Francaise contre
les Myopathies (AFM) in Paris. Tuition is FR 6 000 and the
language of instruction is English. Participants (maximum 24)
must meet the following criteria: (i) be currently affiliated
with an European laboratory, (ii) be familiar with a PC (i.e.
word processing), and (iii) be able to exhibit an immediate need
for linkage mapping. For further information and application
forms, please contact:
Dr. Lynn Davis; AFM; 1 rue de l'Internationale
BP 59 - 91002 EVRY cedex, FRANCE;
telephone: (33)(1) 69 47 28 28, FAX: 60 77 12 16.
3. SOFTWARE NOTES
3.1 Bug in the SLINK program
The following contribution has been submitted by Dr. Weeks
for inclusion in the newsletter:
University of Pittsburgh
Department of Human Genetics
130 DeSoto Street, A300 Crabtree Hall
Pittsburgh, PA 15261
Tel. (412) 624-5388 FAX: (412) 624-3020
WEEKS@PITTVMS.BITNET WEEKS@VMS.CIS.PITT.EDU
1/7/91
To: All users of the SLINK package
From: Daniel E. Weeks
Re: a bug in MSIM, ISIM, and LSIM
Instructions for correcting MSIM, ISIM, and LSIM:
We have discovered another bug in three programs of the SLINK
package. In order to correct this bug, one line in the PROCEDURE
readspseg has to be changed in each of the programs MSIM, ISIM,
and LSIM:
IF j>0 THEN
has to be changed to
IF (j > 0) AND (i <= segperson) THEN
Using a text editor, find the appropriate line in each of your
three source code files (as indicated below) and then change it.
Then you must recompile each corrected program before you use it.
If you have any problems, please feel free to contact me.
Old version:
************************************************
PROCEDURE readspseg;
{Reads from the speedfile in appropriate segments}
VAR
i, j, a, b, sys: integer;
ch : char;
BEGIN {readspseg}
{ Note that each person[]^.unknown is set to FALSE as the
person is read in}
i:=lastspeed;
j:=lastspeed-lastseg;
IF j>0 THEN
BEGIN
person[j]^.unknown:=TRUE;
NEW(person[j]^.store);
{ person[j]^.store:=infoptr(NewPtr(SizeOf(information)));}
WITH person[j]^.store^ DO
FOR sys:=1 TO nlocus DO
FOR a:=1 TO maxall DO
FOR b:=1 TO maxall DO
possible[sys, a, b]:=FALSE;
END;
************************************************
Corrected version:
************************************************
PROCEDURE readspseg;
{Reads from the speedfile in appropriate segments}
VAR
i, j, a, b, sys: integer;
ch: char;
BEGIN {readspseg}
{ Note that each person[]^.unknown is set to FALSE as the
person is read in}
i := lastspeed;
j := lastspeed - lastseg;
IF (j > 0) AND (i <= segperson) THEN
BEGIN
person[j]^.unknown := TRUE;
NEW(person[j]^.store);
{ person[j]^.store := infoptr(NewPtr(SizeOf(information)));}
WITH person[j]^.store^ DO
FOR sys := 1 TO nlocus DO
FOR a := 1 TO maxall DO
FOR b := 1 TO maxall DO
possible[sys, a, b] := FALSE;
END;
************************************************
3.2 Computer programs for human genetic linkage analysis
There has not been much change regarding the LINKAGE
programs since the last Newsletter, except that version 5.1 has
just arrived from Mark Lathrop. We are in the process of
carrying out a few tests and hope to have this latest version
ready for distribution soon.
A particular version of the LINKAGE programs is now
available, which allows for two loci to be jointly responsible
for occurrence of a disease (DISK22 in list of programs). To
receive a list of all our programs please write, fax, or send an
e-mail message.
We are planning on making our programs available by e-mail.
One possibility of doing this would be to install a file server
on our IBM mainframe running under VM/CMS, which is a Bitnet
node. However, we have no file server available and might have
to write one. Does anyone have experience with such programs?
The other possibility is to run a microcomputer under Kermit in
server mode so that people can call up and download information
and program files. The latter solution would be relatively easy
to implement but requires people to pay telephone tolls.
Introductory Linkage Course
Wednesday through Saturday, May 15-18, 1991
Course Description and Prerequisites
This course is intended for researchers without or with only
little prior knowledge of linkage programs. However, familiarity
with the principles of linkage analysis and with the use of IBM
PCs will be required. The course will begin with a brief
introduction to theory and techniques. The main part will
consist of problem-solving sessions with use of computer programs
(LINKAGE, Linkage Utility Programs) and general question-and-
answer sessions. The topics to be covered include strategies and
methods of linkage analysis; reduced penetrance; application of
computer programs (LINKAGE, Linkage Utility Programs);
affecteds-only analyses; inbreeding loops; simple risk
calculations. Computer programs can be taken home (on 3-1/2" or
5-1/4" diskettes). A copyrighted course manual will be mailed
for study before the course begins. Please distribute copies of
this course announcement to anyone interested.
The course will be taught by myself and my collaborators.
It will take place in the computer classroom of the Health
Sciences Library (701 West 168th Street) which is equipped with
20 microcomputers of type IBM PS/2 (3-1/2" diskette drives). Due
to space limitations, course attendance is limited to 30
participants. Participants should plan on arriving in New York
on the evening of Tuesday, May 14, 1991.
Course Fee
The fee for the 4-day course is $500 for researchers at an
academic institution, and $600 for individuals from private (for
profit) companies. It may be paid by check drawn on a U.S. bank
made payable to Columbia University Dept. of Psychiatry, by
Government pay order, or by Travellers checks, but send no money
now -- applicants will receive an invoice with detailed
instructions. As there is presently no support for this course
from sources other than the course fee, no reduction of the cost
to applicants is possible. This fee covers tuition and course
related expenses (handouts, diskettes, rental of classroom etc.)
but not room, board or meals. Course participants will receive a
list of good and moderately priced hotels in New York and will
have to make their own arrangements (except foreign
participants). A small number of guest rooms are available in
Bard Hall next to the Health Sciences Library (double rooms at
$65 per room per night, single rooms at $60).
Application for Linkage Course by Dr. Jurg Ott
Please fill out this page and send it by mail or,
preferably, by FAX (see below). People interested in staying in
a double room at Bard Hall should indicate a preferred roommate,
or else we will match applicants. PLEASE PRINT.
Your name:
Affiliation:
Address:
Tel. number:
FAX number:
Bitnet:
Interested in staying at Bard Hall? YES / NO DOUBLE / SINGLE
If yes, which nights? Tue Wed Thu Fri Sat Sun
What size diskettes do you use? 3-1/2" 3-1/2"HD 5-1/4"HD
(we prefer 3-1/2"; we have no easy way of writing to low-density
5-1/4" disks)
For applicants from abroad: Do you want us to make hotel reserva-
tions? What accommodations?
Below, please describe which linkage programs you have used if
any, how many families you have analyzed, and other experience in
linkage analysis you might have:
Signature:
Date:
Katherine Montague, Course Coordinator
Tel. (212) 960-2507
FAX +1 (212) 568-2750 or 960-5624
Bitnet: OTT@NYSPI